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401 results for “nuclear gene”
Data from: Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low-copy nuclear genes
DNA sequence data from the low-copy nuclear genes waxy (GBSSI) and leafy were compared with plastid sequence data from prior studies to reconstruct phylogenetic relationships in the Wintergreen Group of tribe Gaultherieae (Ericaceae). We conducted phylogenetic analysis with 109 species that includes representatives of all 15 major clades previously diagnosed in the Wintergreen Group and that together span its circum-Pacific distribution. Results yielded two distinct homeologous copies of waxy for two of the clades, each in widely separated parts of the tree. It also yielded two copies of leafy for one of the clades; only one copy of leafy was found for the other clade, but it was placed in the same major clade as its waxy counterpart and well away from its placement in a prior plastid analysis. A combined four-locus (waxy, leafy, ITS, and plastid loci) phylogenetic analysis of all available relevant data placed the copies of each of the clades in two distinct positions in the phylogeny with strong overall statistical support. In combination with evidence from morphology, reproductive biology, and cytology, the results suggest that these clades arose through allopolyploid hybridization between lineages deep in the phylogeny but relatively close geographically. This finding confirms previous assumptions that hybridization plays an important role in the evolution of the Gaultherieae.
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Set of 4 597 baits designed in collaboration with RapidGenomics (Gainesville, Florida, USA) to capture the identified low‐ to single‐copy nuclear genes (LSCN).
<p>This dataset presents a set of 4,597 baits designed in collaboration with RapidGenomics (Gainesville, Florida, USA) to capture the identified low- to single-copy nuclear genes (LSCN) in our study. These baits were instrumental in our research on the evolutionary relationships of the Neotropical magnolias based on plastome and nuclear phylogenomics. The data provided are crucial for understanding the methodology and results of our study.</p>
Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome
<p>The data set is the result of genetic inventory on 1970 Pedunculate oak trees from 197 locations in Europe. The samples are from the countries: Belarus, Bosnia, Bulgaria, Croatia, Finland, France, Germany, Hungary, Italy, Latvia, Poland, Russia and Ukraine. At each location ten individual trees were collected. The data set includes the location ID and geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs and five mitochondrial SNPs).</p> <p>The genotype of each individual is one row in the csv-file "genotypes". The genotypes at the nuclear markers are diploid and represented by two columns per gene marker. The genetic information at the organelle genome is haploid. For each of these gene markers one column is used. Genotypes are coded by Arabic numbers. The meaning of the numbers is explained in the table "coding genotypes" in a second csv-file.</p>
Alignments used for the phylogenies in "Caryophylliids (Anthozoa, Scleractinia) have a mitochondrial gene rearrangement: lesson learned from mitochondrial and nuclear phylogenomics"
<p>"mitochondrial_caryotree.phy": concatenated alignment of mitochondrial data in phylip format; "mitochondrial_caryotree.partitions.txt": indication of start/stop positions of each partition in the mitochondrial data alignment; "nuclear_caryotree_55taxa-50p.phylip": alignment of nuclear exons and ultraconserved elements in phylip format.</p>
Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome
<p>The data set is the result of genetic inventory on 970 Pedunculate oak trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern part of the natural species range. The data set includes the sample IDs, geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a set of 385 gene markers covering the nuclear (n=364) and the organelle genomes (chloroplast: n=14, mitochondria: n=7) by use of a genotyping by sequencing approach. With exception of three INDELs (Insert and Deletion mutations) all gene markers are SNPs (Single nucleotide Polymorphism).</p>
Nuclear phylogeography reveals strong impacts of gene flow in big brown bats
<p><strong>Aim: </strong>Understanding speciation mechanisms requires disentangling processes that promote and erode population-level divergence. Three hypotheses are raised that contemporary population structure is mainly shaped by refugial divergence, post-glacial gene flow, or combined effects of both. Testing these hypotheses requires range-wide phylogeography and integrative analyses across scales. Here we aim to 1) re-estimate the previously unresolved nuclear phylogeography of a widespread bat; 2) test the above three phylogeographic hypotheses; and 3) inform conservation management under climate change.</p> <p><strong>Location: </strong>North America including Caribbean.</p> <p><strong>Taxon: </strong>The big brown bat (<em>Eptesicus fuscus</em>).</p> <p><strong>Methods:</strong> We collected range-wide samples and genome-wide markers using restriction site-associated DNA sequencing. Population structure was analyzed by clustering methods and spatial estimations. Nuclear phylogeography was estimated using tree methods (concatenation and coalescent) and network analyses (TreeMix). Phylogeographic hypotheses were tested by comparing alternative evolutionary scenarios using demographic modeling. Species distribution modeling was used to help identify Pleistocene refugia and predict future range shifts under climate change.</p> <p><strong>Results: </strong>We identified three populations in the Caribbean, Eastern, and Western North America. The west population further split into three phylogeographic clades in Pacific, Southwestern North America, and Mexico. Discordances among mitochondrial and nuclear topologies reflected strong impacts of gene flow without sex biases. Demographic modeling supported scenarios of historical isolation followed by secondary gene flow and estimated Holocene divergence time. Species distribution was overall continuous during glaciation with possible regional isolation, and northward range shifts were predicted under future climate change.</p> <p><strong>Main Conclusions: </strong>Our results supported the hypothesis that combined effects of historical isolation and secondary gene flow shaped the contemporary population divergence. We showed that climate change probably triggered the initial divergence and that gene flow has strong impacts on the observed nuclear phylogeography. Our empirical study demonstrates dynamic within-species processes generating the population divergence that predates speciation.</p>
Data from: Low-copy nuclear genes reveal new evidence of incongruence in relationships within Malvaceae s.l.
<p>The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s.l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plant Project (1KP) and publicly available genome information from cotton, cacao, and <i>Arabidopsis, </i>we designed a set of molecular markers of potentially single-or low-copy nuclear genes for Malvaceae s.l. Phylogenetic potential of these new loci was compared to previously applied conventional markers (i.e., plastid <i>trnK</i>-<i>matK</i> region and <i>rbcL</i> gene and the <a>nrDNA </a>ITS region) using the phylogenetic informativeness method. The results show that, when the mined nuclear regions are used in combination, it is possible to resolve relationships at different taxonomic levels within the phylogeny. However, incongruence among nuclear loci is frequent in the group, explaining the prevalence of unresolved phylogenetic relationships.</p>
Concatenated amino acid (AA) phylogenetic dataset of nuclear gene orthologs for Ephydroidea (Diptera)
<p>The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. Extraordinary diversity in life histories, feeding habits, and morphology are hallmarks of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm the placement of Cryptochetidae as a sister taxon to a large clade containing both Drosophilidae and Braulidae – the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.</p>
Fig. 1 in Phylogenetic analysis of the Common Krait (Bungarus caeruleus) in Pakistan based on mitochondrial and nuclear protein coding genes
Fig. 1. Sample collection sites in Pakistan for Common Krait (Bungarus caeruleus).
Fig. 3 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 3. Continues. For caption, see next part.
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
<p>With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage <i>in silico</i>. We tested the performance of four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the <i>Vitis</i> clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large datasets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach.</p>
Phylomitogenomics reveals mito-nuclear concordance in social wasps: the performance of mitochondrial markers and gene order for hymenopteran systematics.
<p>Mitochondrial (mtDNA) genes have served as widely utilized genetic loci for animal phylogenetics and phylogeography studies. However, the phylogenetic performance of many mtDNA genes has not been empirically evaluated across lineages within hymenopteran wasps. To address this question, we assembled and analyzed mitogenomic data from social wasps, representing the four recognized tribes of Polistinae and also all Epiponini genera. Additionally, we evaluated whether mtDNA gene order in Polistinae is congruent with its tribal classification. Using concatenation phylogenetic methods, we show phylogenetic congruence between mitogenomic and nuclear data. Statistically comparing the phylogenetic performance of individual mtDNA genes, we demonstrate that for social wasps the molecular markers COI, 16S, NAD5, and NAD2 perform best, while ATP6, COII, and 12S show the worst results. Finally, we verified that the tRNA cluster close to the noncoding region is a hotspot of rearrangement in Vespidae and can be used as additional information for the systematics of this group. Together, these results indicate that mitogenomes contain robust phylogenetic signal to elucidate the evolutionary history of Vespidae. Moreover, our study identifies the best choice of mitochondrial markers for systematic investigations of social wasps.</p>
Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes
<p><span>Mulberry (genus <em>Morus</em>), belonging to the order Rosales, family Moraceae, is an important woody plant due to its economic value in sericulture as well as for its nutritional benefits and medicinal values. However, the taxonomy and phylogeny of <em>Morus</em> remain challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of <em>Morus</em>, we combined plastomes and a large-scale nuclear gene to investigate their phylogenetic relationships in the present study. We assembled the plastomes and screened 211 single-copy nuclear genes from 14 <em>Morus</em> species and related taxa. The plastomes of <em>Morus</em> species were relatively conserved in terms of genome size, gene content and order, IR boundary and codon usage. Using nuclear data, we yielded completely identical topologies based on coalescent and concatenation methods, and multiple individuals of the same species were intraspecific monophyletic. The genus <em>Morus</em> was supported as a monophyly, and <em>M. notabilis</em> was recovered as the first diverging, and the two North American <em>Morus</em> species, <em>M. celtidifolia</em> and <em>M. rubra</em>, were sister to the other Asian species. However, the relationships of <em>Morus</em> based on plastomes were strongly incongruent with those from nuclear genes, and intraspecific non-monophyly was retrieved in the plastid phylogeny. Comparisons of nuclear and plastid phylogenies, and combining with the result of network inference, hybridization/introgression was regarded as the main cause of the discordance between nuclear and plastid phylogenies in the genus <em>Morus</em>. Overall, the robust phylogenetic relationships of <em>Morus</em> described here will be useful for genetic resources development of this economically important genus and exploitation of sericulture industry.</span></p>
Data from: Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes
<p>Polyploids represent a new frontier in species discovery among embryophytes. Within mosses, polyploid discovery is challenged by low morphological complexity. The rapid expansion of sub-genome sequencing approaches in addition to computational approaches to identifying whole genome duplication using allelic variation among nuclear markers has allowed for increased polyploid discovery among mosses. We confirm the intergeneric hybrid nature of <em>E. hungaricus</em>, and the allopolyploid origin of <em>P. eurystomum </em>and of one population of <em>P. collenchymatum</em>. We also reveal that hybridization gave rise to <em>P. immersum, </em>as well as to yet unrecognized lineages sharing the phenotype of <em>P. pyriforme</em>,<em> P. sphaericum</em> and <em>P. collenchymatum. </em>Our findings and methods demonstrate the utility of a novel approach to allele phasing and subgenome assignment, called homologizer, when working with polyploid genomes, and its value in identifying progenitor species using target capture data.</p>
Data from: Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes
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Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome
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Data from: Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low-copy nuclear genes
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Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome
Open the record for dataset details and reuse information.
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
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